Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

33 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of differentially-expressed genes in Tg(actb2:KIT-D816V) transgenic zebrafish versus wild-type adult kidneys

ABSTRACT: Transcriptional profiling of pooled adult kidneys from transgenic zebrafish expressing human KIT-D816V mutant gene versus wild-type zebrafish was performed. The aim of this experiment was to determine the expression and cellular changes caused by expression of KIT-D816V oncogene in the hematopoietic organ in zebrafish. This transgenic zebrafish represents a model of systemic mastocytosis with many features of this disease present in adults Two-condition experiment, Tg(actb2:KIT-D816V) versus wild-type(AB), one replicate of each prepared from 3 adult kidneys of each genotype and a dye-swap hybridization of these RNA samples.

ORGANISM(S): Danio rerio

SUBMITTER: Sergey Prykhozhij

PROVIDER: E-GEOD-54614 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Tg(actb2:KIT-D816V) transgenic zebrafish versus wild-type at 28 hpf

Project description:Transcriptional profiling of 28 hpf zebrafish transgenic expressing human KIT-D816V mutant gene versus wild-type embryos was performed. The aim of this experiment was to determine the expression changes caused by expression of KIT-D816V oncogene. This transgenic zebrafish represents a model of systemic mastocytosis with many features of this disease present in adults, but no very clear phenotypes in embryos. Thus, we attempted to determine if there are certain expression changes, which can be used as molecular features of active KIT expressed in these embryos. Two-condition experiment, Tg(actb2:KIT-D816V) versus wild-type(AB), 4 replicate experiments with a dye-swap each time

2014-02-03 | E-GEOD-54613 | biostudies-arrayexpress

Microarray analyses of transgenic zebrafish expressing human KIT-D816V gene versus wild-type zebrafish

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-02-03 | E-GEOD-54615 | biostudies-arrayexpress

Transgenic NUP98-HOXA9 Zebrafish Embryos: Unactivated ('lGl') vs. Cre-activated ('NHA9')

Project description:Transcriptional profiling of zebrafish embryos at 28 hours post fertilization, comparing control 'unactivated' Tg(spi1::lox-eGFP-lox::NHA9) embryos with experimental 'Cre-activated' Tg(spi1::NHA9) embryos. Goal was to determine the effects of expressing NUP98-HOXA9 oncogene on global and blood cell-specific gene expression in early zebrafish development. Two-condition experiment, unactivated 'lGl' embryos vs. Cre-activated 'NHA9' embryos. Biological replicates: 2 control replicates, 2 experimental replicates.

2014-10-30 | E-GEOD-62793 | biostudies-arrayexpress

Overexpression of wnt8b and dkk1b in zebrafish empryos

Project description:To investigate its role during zebrafish development, wnt signalling was either activated by the conditional expression of wnt8b or inhibited by the conditional expression of dickkopf-1b (dkk1b) under the control of the hsp70 heat shock promoter. The transgenic constructs contained a gfp reporter fusion to differentiate between transgenic embryos and their wild type siblings. Transgenic embryos and wild type control embryos at the 48 hours post fertilization stage (hpf) were exposed to heat shock (37 C) for 2 hours and were collected 4 hours after heat shock. The transcriptional response to activated or inhibited wnt signalling was profiled using microarrays and compared to wild type expression.

2013-11-14 | E-MTAB-1887 | biostudies-arrayexpress

Zebrafish transgenerational methylation profiling in response to TCDD, 5-AZA and MeHg

Project description:Adult F0 female zebrafish were fed with control diet or diets containing 5-AZA, MeHg or TCDD. After breeding with unexposed males to produce the F1 generation, livers were sampled from the F0 females. F1 generation embryos were unexposed to test chemicals, were sampled, then bred to produce F2 fish, also unexposed to test chemicals. Methylated DNA immunoprecipitation was carried out on liver samples from F0 and F1 and F2 embryos and MeDIP samples were labeled with Cy5 and hybridised to a zebrafish CGI tiling array versus Cy3-labled zebrafish genomic DNA. The objective was to determine DNA methylation changes following chemical exposure and whether these persisted transgenerationally.

2014-03-01 | E-MTAB-2057 | biostudies-arrayexpress

Transcriptomic analysis reveals the involvement of canonical Wnt signaling in zebrafish gonad differentiation

Project description:Zebrafish males undergo a juvenile ovary to testis type gonadal transformation process. To understand how juvenile ovary-to-testis transformation in zebrafish is genetically regulated, we compared the transcriptomes of juvenile ovary (JO) and juvenile ovotestis (JOT) samples at 35 dpf using the Gonad Uniclone Microarray v1 (ArrayExpress ID: A-MEXP-838). We also analyzed the transcriptomes of the 32 dpf JO, 32 dpf JOT, 34 dpf JOT, and 36 dpf JOT gonads using the slightly modified Gonad Uniclone Microarray v2 and together with the 35 dpf JO and 35 dpf JOT samples, compared the JO samples against the JOT samples to identify genes that could be potentially involved in the gonad transformation process.

2013-12-27 | E-MEXP-3879 | biostudies-arrayexpress

Comparative oncogenomic analysis of copy number alterations in human and zebrafish tumors enables cancer driver discovery

Project description:The identification of cancer drivers is a major goal of current cancer research. Finding driver genes within large chromosomal events is especially challenging because such alterations encompass many genes. Previously, we demonstrated that zebrafish malignant peripheral nerve sheath tumors (MPNSTs) are highly aneuploid, much like human tumors. In this study, we examined 147 zebrafish MPNSTs by massively parallel sequencing and identified both large and focal copy number alterations (CNAs). Given the low degree of conserved synteny between fish and mammals, we reasoned that comparative analyses of CNAs from fish versus human MPNSTs would enable elimination of a large proportion of passenger mutations, especially on large CNAs. Accordingly, we found less than one third of the human CNA genes were co-gained or co-lost in zebrafish, dramatically narrowing the list of candidate cancer drivers for both focal and large CNAs. We conclude that zebrafish-human comparative analysis represents a powerful, and broadly applicable, tool to enrich for evolutionarily conserved cancer drivers. --- This filing comprises data related to GEO entry GSE23666 ("Highly Aneuploid Zebrafish Malignant Peripheral Nerve Sheath Tumors have Genetic Alterations Similar to Human Cancers"), representing a followup study. 147 pairs of zebrafish (Danio rerio) tumor (MPNST) and normal tail control samples

2013-12-31 | E-GEOD-38397 | biostudies-arrayexpress

Transcription profiling of rac1 knock-down zebrafish embryos

Project description:Phenotypic, proteome and transcriptome analysis of rac1 knockdown in zebrafish embryos

2008-12-31 | E-MEXP-1593 | biostudies-arrayexpress

Zic3 interacts with distant regulatory elements to regulate zebrafish developmental genes

Project description:Zic3 regulates early embryonic patterning in vertebrates. Its loss-of-function disrupts gastrulation, left-right patterning, and neurogenesis. We use the zebrafish as a model to study the developmental role of Zic3 in vivo. Using a combination of two genomics approaches – ChIP-seq and microarray, we identified Zic3 targets, which include genes from the Nodal and Wnt pathways, and show for the first time cis-regulation of these genes by Zic3 using in vivo enhancer assay. We uncovered a previously unrecognized link between Zic3 and the non-canonical Wnt pathway in gastrulation and left-right patterning, and identified neural pre-pattern genes as Zic3 targets during the early steps of neural induction. Zic3 preferably binds to distal intergenic regions, some of which contain evolutionarily conserved functional enhancers. Our study establishes the zebrafish as an excellent model for genome-wide study of a transcription factor in vivo. Zic3 ChIP of wild type and sqet33 transgenic

2014-02-27 | E-GEOD-41458 | biostudies-arrayexpress

Zebrafish larvae submitted to simulated microgravity on a clinostat (CLINO) at 5dpf for one day

Project description:The general objective of the study was to determine modulation of gene expression by environmental factors, specifically simulation of microgravity, with a special emphasis on bone formation. For this reason, the specific period of treatment was chosen between 5-6 days post-fertilization (dpf), when bone formation and calcification are taking place. Zebrafish larvae were placed at 5 dpf into a clinostat (CLINO) for 24 hours, which was shown to simulate microgravity by the specific rotational movements it generates. We show that CLINO exposure causes a clear decrease of bone formation, as illustrated by cranial skeleton staining of the bone matrix by Alizarin Red, by morphometric analysis of the resulting images. Thus, a whole genome micro-array experiment was conducted to identify genes that may be involved in the observed effect on bone formation.

2016-02-15 | E-MTAB-4476 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data